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RepeatMaskSplitter.java
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RepeatMaskSplitter.java
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/*
* The MIT License (MIT)
*
* Copyright (c) 2016 University of California San Diego
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*
*
*/
package org.broad.igv.tools;
import org.broad.igv.Globals;
import org.broad.igv.util.ParsingUtils;
import htsjdk.tribble.readers.AsciiLineReader;
import java.io.*;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.Properties;
/**
* Splits a repeat mask file downloaded from UCSC into multiple files, one per repeat class.
* Assumes downloaded columns as follows (use table browser, and "select columns" option
* <p/>
* genoName genoStart genoEnd strand repName repClass repFamily
* <p/>
* Assumes file is sorted by chromosome
*
* @author jrobinso
*/
public class RepeatMaskSplitter {
public static void main(String[] args) {
File file = new File(args[0]);
split(file);
}
public static void split(File inputFile) {
int binCol = 0;
int millDivCol = 2;
int millDelCol = 3;
int millInsCol = 4;
int chrCol = 5;
int startCol = 6;
int endCol = 7;
int strandCol = 9;
int nameCol = 10;
int classCol = 11;
int famCol = 12;
Map<String, LinkedHashMap<String, String>> fileMappings = new HashMap();
AsciiLineReader reader = null;
HashMap<String, PrintWriter> writers = new HashMap();
PrintWriter allWriter = null;
try {
reader = new AsciiLineReader(new FileInputStream(inputFile));
// Skip header
reader.readLine();
String nextLine;
File dir = inputFile.getParentFile();
allWriter = new PrintWriter(new BufferedWriter(new FileWriter("rmsk.bed")));
allWriter.println("track name=\"Repeat Masker\" \" gffTags=\"on\"");
while ((nextLine = reader.readLine()) != null) {
String[] tokens = Globals.tabPattern.split(nextLine, -1);
String chr = tokens[chrCol];
String repClass = tokens[classCol];
if (repClass.contains("?")) {
continue;
}
String filename = repClass + ".bed";
// Get or create file writer for the class
PrintWriter pw = writers.get(filename);
if (pw == null) {
File outputFile = new File(dir, filename);
pw = new PrintWriter(new BufferedWriter(new FileWriter(outputFile)));
pw.println("track name=\"" + repClass + "\" gffTags=\"on\"");
writers.put(filename, pw);
}
String nm = tokens[nameCol];
String fam = tokens[famCol];
String name = "Name=" + nm + ";Class=" + repClass + ";Family=" + fam;
pw.print(chr);
pw.print("\t");
pw.print(Integer.parseInt(tokens[startCol]));
pw.print("\t");
pw.print(Integer.parseInt(tokens[endCol]));
pw.print("\t");
pw.print(name);
pw.print("\t");
pw.print(tokens[strandCol]);
pw.println();
allWriter.print(chr);
allWriter.print("\t");
allWriter.print(Integer.parseInt(tokens[startCol]));
allWriter.print("\t");
allWriter.print(Integer.parseInt(tokens[endCol]));
allWriter.print("\t");
allWriter.print(name);
allWriter.print("\t");
allWriter.print(tokens[strandCol]);
allWriter.println();
}
} catch (Exception e) {
e.printStackTrace();
} finally {
reader.close();
// allWriter.close();
closeWriters(writers);
}
}
private static void closeWriters(HashMap<String, PrintWriter> writers) {
for (PrintWriter pw : writers.values()) {
pw.close();
}
writers.clear();
}
}